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mmu_circRapgef6_789
Basic information of circular RNA
PanCircBase ID:
mmu_circRapgef6_789
mm39_Chr. Position ID:
chr11|54516686|54527041|+
Gene name:
Rapgef6
Transcript:
ENSMUST00000102743.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,11,12,13,14
Exon/intron offsets:
0,724,5331,8899,10151
Genomic length:
10355
Exon/intron sizes in nt:
15,91,53,16,51,08,204
Flanking exon/introns:
chr11:54513278-54516686|chr11:54527041-54530575
Splice length:
789
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTTGACTCATGGTATGTCATTTTAAATGGCACTGTAGAAATTAGTCATCCAGATGGGAAAATAGAAAATCTCTTCATGGGAAATAGTTTTGGGATTGTCCCCACGCTGGATAAGCAGCACATGCATGGAGCTGTCAGGACCAAAGTCGATGATTGTCAGTTTGTCTGCATAGCTCAACAAGACTATTGGAGAATTTTAAATCATGTGGAAAAAAATACTCACAAAGTTGAGGAAGAGGGAGAGATTGTCATGGTACATGAGCACCGTGAGCTAGACCGGAGCGGAACCAGGAAAGGACACATTGTAATCAAGGCAACACCTGAGCGTCTCATCATGCATTTGATAGAAGAACATTCTATTGTGGACCCAACATACATAGAAGATTTCCTCTTAACTTACAGGACATTTCTTGAAACTCCTTTGGATGTTGGGATCAAGCTTTTGGAATGGTTTAAGATTGACAACCTAAGGGATAAGGTGACACGGATTGTACTCTTATGGGTAAATAATCATTTTAATGATTTTGAAGGTGATCCTGCTATGACTCAATTTCTAGAAGAATTTGAAAGAAATTTGGAAGATACAAAAATGAATGGTCACCTCAGGTTATTGAATATTGCCTGTGCTGCAAAGGCTAAGTGGAGGCAAGTTGTACTGCAGAAGGCGTCCCGTGAGTCCCCGCTGCACTTCTGCCTTACTGGGGGCAGTGAGAAGGGATTTGGAGTCTTTGTTGAAGAAGTAGAATCTGGTAGCAAAGCTGCTGACGCAGGACTGAAAAGGGGTGATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGCAGTGAGAAGGGATTT
59.67
TGGATGACTAATTTCTACAGTGCCA
60.05
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGCAGTGAGAAGGGATTT
59.67
TGGATGACTAATTTCTACAGTGCC
58.57
140
PCR template sequence:
CTGCCTTACTGGGGGCAGTGAGAAGGGATTTGGAGTCTTTGTTGAAGAAGTAGAATCTGGTAGCAAAGCTGCTGACGCAGGACTGAAAAGGGGTGATCAGCTTGACTCATGGTATGTCATTTTAAATGGCACTGTAGAAATTAGTCATCCAGATGGGAAAATAGAAAATCTCTTCATGGGAAATAGTTTTGGGATTGTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-139-5p(1), mmu-miR-324-3p(1), mmu-miR-297a-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGGGGTGATCAGCTTGACTCATGGT
siRNA sets
CATGAGTCAAGCTGATCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPGEF6_789_ORF_1
1.0437
0.064851278
0.999578899
1503
ORF sequence:
ATGGGAAATAGTTTTGGGATTGTCCCCACGCTGGATAAGCAGCACATGCATGGAGCTGTCAGGACCAAAGTCGATGATTGTCAGTTTGTCTGCATAGCTCAACAAGACTATTGGAGAATTTTAAATCATGTGGAAAAAAATACTCACAAAGTTGAGGAAGAGGGAGAGATTGTCATGGTACATGAGCACCGTGAGCTAGACCGGAGCGGAACCAGGAAAGGACACATTGTAATCAAGGCAACACCTGAGCGTCTCATCATGCATTTGATAGAAGAACATTCTATTGTGGACCCAACATACATAGAAGATTTCCTCTTAACTTACAGGACATTTCTTGAAACTCCTTTGGATGTTGGGATCAAGCTTTTGGAATGGTTTAAGATTGACAACCTAAGGGATAAGGTGACACGGATTGTACTCTTATGGGTAAATAATCATTTTAATGATTTTGAAGGTGATCCTGCTATGACTCAATTTCTAGAAGAATTTGAAAGAAATTTGGAAGATACAAAAATGAATGGTCACCTCAGGTTATTGAATATTGCCTGTGCTGCAAAGGCTAAGTGGAGGCAAGTTGTACTGCAGAAGGCGTCCCGTGAGTCCCCGCTGCACTTCTGCCTTACTGGGGGCAGTGAGAAGGGATTTGGAGTCTTTGTTGAAGAAGTAGAATCTGGTAGCAAAGCTGCTGACGCAGGACTGAAAAGGGGTGATCAGCTTGACTCATGGTATGTCATTTTAAATGGCACTGTAGAAATTAGTCATCCAGATGGGAAAATAGAAAATCTCTTCATGGGAAATAGTTTTGGGATTGTCCCCACGCTGGATAAGCAGCACATGCATGGAGCTGTCAGGACCAAAGTCGATGATTGTCAGTTTGTCTGCATAGCTCAACAAGACTATTGGAGAATTTTAAATCATGTGGAAAAAAATACTCACAAAGTTGAGGAAGAGGGAGAGATTGTCATGGTACATGAGCACCGTGAGCTAGACCGGAGCGGAACCAGGAAAGGACACATTGTAATCAAGGCAACACCTGAGCGTCTCATCATGCATTTGATAGAAGAACATTCTATTGTGGACCCAACATACATAGAAGATTTCCTCTTAACTTACAGGACATTTCTTGAAACTCCTTTGGATGTTGGGATCAAGCTTTTGGAATGGTTTAAGATTGACAACCTAAGGGATAAGGTGACACGGATTGTACTCTTATGGGTAAATAATCATTTTAATGATTTTGAAGGTGATCCTGCTATGACTCAATTTCTAGAAGAATTTGAAAGAAATTTGGAAGATACAAAAATGAATGGTCACCTCAGGTTATTGAATATTGCCTGTGCTGCAAAGGCTAAGTGGAGGCAAGTTGTACTGCAGAAGGCGTCCCGTGAGTCCCCGCTGCACTTCTGCCTTACTGGGGGCAGTGAGAAGGGATTTGGAGTCTTTGTTGAAGAAGTAGAATCTGGTAGCAAAGCTGCTGACGCAGGACTGAAAAGGGGTGATCAG
Peptide sequence:
MGNSFGIVPTLDKQHMHGAVRTKVDDCQFVCIAQQDYWRILNHVEKNTHKVEEEGEIVMVHEHRELDRSGTRKGHIVIKATPERLIMHLIEEHSIVDPTYIEDFLLTYRTFLETPLDVGIKLLEWFKIDNLRDKVTRIVLLWVNNHFNDFEGDPAMTQFLEEFERNLEDTKMNGHLRLLNIACAAKAKWRQVVLQKASRESPLHFCLTGGSEKGFGVFVEEVESGSKAADAGLKRGDQLDSWYVILNGTVEISHPDGKIENLFMGNSFGIVPTLDKQHMHGAVRTKVDDCQFVCIAQQDYWRILNHVEKNTHKVEEEGEIVMVHEHRELDRSGTRKGHIVIKATPERLIMHLIEEHSIVDPTYIEDFLLTYRTFLETPLDVGIKLLEWFKIDNLRDKVTRIVLLWVNNHFNDFEGDPAMTQFLEEFERNLEDTKMNGHLRLLNIACAAKAKWRQVVLQKASRESPLHFCLTGGSEKGFGVFVEEVESGSKAADAGLKRGDQ
IRESfinder result
IRESfinder score
0.616138895
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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